Improving bread quality using Deinococcus geothermalis glycogen branching enzyme

Glycogen branching enzyme(GBE) catalyzes transglycosylation reaction producing α-1,6-glucosidic linkages by cleaving an α-1,4-glucosidic linkage. Deinococcus geothermalis GBE (DgGBE) has the unique activity to form a large number of short oligosaccharide side chains(degree of polymerization 3~5) from the reaction with amylose. To observe the influence of DgGBE on bread quaility, we added 100 unit of the enzyme per kg of the flour at the step of mixing dough. During the fermentation, DgGBE treated dough showed 50~100% larger volume than control. After baking, the total volume and the specific volume of DgGBE treated loaf showed about 10% larger than those of control. The baked breads were sliced to 2cm of depth and stored in 25 degrees celcius, and then the texture was evaluated by texture analyzer during storage time. Hardness and Chewiness of DgGBE treadted bread increased slowly to compared with those of the control. DgGBE treated bread showed a significant effect on antistaling. 1. Shupeng Wua, Yu Liu , Qiaojuan Yan , Zhengqiang Jiang (2014) Gene cloning, functional expression and characterisation of a novel glycogen branching enzyme from Rhizomucor miehei and its application in wheat breadmaking. Food Chemistry 159 (2014) 85-94 2. José Manuel Amigo , Arantxa del Olmo Alvarez , Merete Møller Engelsen , Henrik Lundkvist , Søren Balling Engelsen (2016) Staling of white bread crumb and effect of maltogenic α-amylases. Part 1 : Spatial distribution and kinetic modeling of hardness and resilience. Food Chemistry 208 (2016) 318-32

Development of screening method for the selection of mutants to improve the substrate specificity of Pyrococcus furiosus thermostable amylase

Pyrococcus furiosus thermostable amylase (PFTA) shows the activities of both a cyclodextrin hydrolyzing enzyme and an α-amylase. To improve the substrate affinity and hydrolyzing activity against cyclodextrins, the saturation mutagenesis on the residue of PFTA active site was carried out. After the mutagenesis, the new screening method was needed to select appropriate mutants efficiently from various mutants. Among the α-, β-, γ-cyclodextrins, only β-cyclodextrin makes the complex with phenolphthalein. When added the β-cyclodextrin into phenolphthalein reagent, the color of the solution was changed red to colorless under alkaline condition. In this study, we developed screening method by using 24-well plate and phenolphthalein to compare the activity of PFTA mutants. Escherichia coli MC1061 was used as a host for the expression of various recombinant plasmids and cultured in 24-well plate with Luria-Bertani broth containing kanamycin. After cell lysis by heat treatment, each cell extracts were reacted with β-cyclodextrin at 70℃. Reacted mixtures were put into 96-well plate with NaOH solution and then add the phenolphthalein reagent respectively. Lastly, the absorbance of the mixture was measured at 550 nm. The substrate specificity of PFTA mutants was compared from the difference of absorbance. References 1. Sung-Jae Yang, Hee-Seob Lee, Cheon-Seok Park, Yong-Ro Kim, Tae-Wha Moon, and Kwan-Hwa Park. 2004. Enzymatic Analysis of an Amylolytic Enzyme from the Hyperthermophilic Archaeon Pyrococcus furiosus Reveals Its Novel Catalytic Properties as both an α-Amylase and a Cyclodextrin-Hydrolyzing Enzyme. APPL. ENVIRON. MICROBIOL. 70:5988-5995 2. Anuj Goel, Sanjay N. Nene. 1995. Modifications in the Phenolphthalein Method for Spectrophotometric Estimation of Beta Cyclodextrin. Starch/Starke. 47:399-40

The Grind for Good Data: Understanding ML Practitioners' Struggles and Aspirations in Making Good Data

We thought data to be simply given, but reality tells otherwise; it is costly, situation-dependent, and muddled with dilemmas, constantly requiring human intervention. The ML community's focus on quality data is increasing in the same vein, as good data is vital for successful ML systems. Nonetheless, few works have investigated the dataset builders and the specifics of what they do and struggle to make good data. In this study, through semi-structured interviews with 19 ML experts, we present what humans actually do and consider in each step of the data construction pipeline. We further organize their struggles under three themes: 1) trade-offs from real-world constraints; 2) harmonizing assorted data workers for consistency; 3) the necessity of human intuition and tacit knowledge for processing data. Finally, we discuss why such struggles are inevitable for good data and what practitioners aspire, toward providing systematic support for data works

A Qualitative Study on the Difference in Organizational Fit of IT Supporting Organizations

For many years, factors that increase the competitive advantage of organizations have been studied in organizational research. For an Information Technology (IT) organization, the main issues are the fitness of the IT and organization strategies and methods for revitalizing IT knowledge management (Earl, 2001; Rathnam, Johnsen, & Wen, 2005; Zack, 2002). However, there are few studies that have evaluated the competitiveness of an organization with reference to the correspondence of these constituent factors with organizational objectives. In this research a multi-contingency view was applied to Korean agencies, and the regional agencies with good performance and those with poor performance were compared with regard to this measure of fitness. The results of this study confirmed that the regions that received a favorable evaluation from experts exhibited good fit overall, and the constituent parts of the organization were consistent with the firm’s objectives

Structural dynamics and divergence of the polygalacturonase gene family in land plants

A distinct feature of eukaryotic genomes is the presence of gene families. The polygalacturonase (PG) (EC3.2.1.15) gene family is one of the largest gene families in plants. PG is a pectin-digesting enzyme with a glycoside hydrolase 28 domain. It is involved in numerous plant developmental processes. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Here, phylogenetic and gene structure analysis of PG genes in algae and land plants revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. PG genes in land plants contained 15 homologous intron blocks and 13 novel intron blocks. Intron position and phase were not conserved between PGs of algae and land plants but conserved among PG genes of land plants from moss to vascular plants, indicating that the current introns in the PGs in land plants appeared after the split between unicellular algae and multicelluar land plants. These findings demonstrate that the functional divergence and differentiation of PGs in land plants is attributable to intronic loss. Moreover, they underscore the importance of intron gain and loss in genomic adaptation to selective pressure

Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization

BACKGROUND: Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups. RESULTS: We investigated the molecular characteristics of genetic changes variation of thymoma using cDNA microarray based-comparative genomic hybridization (CGH) with a 17 K cDNA microarray in an indirect, sex-matched design. Genomic DNA from the paraffin embedded 39 thymoma tissues (A 6, AB 11, B1 7, B2 7, B3 8) labeled with Cy-3 was co-hybridized with the reference placenta gDNA labeled with Cy-5. Using the CAMVS software, we investigated the deletions on chromosomes 1, 2, 3, 4, 5, 6, 8, 12, 13 and 18 throughout the thymoma. Then, we evaluated the genetic variations of thymoma based on the subgroups and the clinical behavior. First, the 36 significant genes differentiating five subgroups were selected by Significance Analysis of Microarray. Based on these genes, type AB was suggested to be heterogeneous at the molecular level as well as histologically. Next, we observed that the thymoma was divided into A, B (1, 2) and B3 subgroups with 33 significant genes. In addition, we selected 70 genes differentiating types A and B3, which differ largely in clinical behaviors. Finally, the 11 heterogeneous AB subtypes were able to correctly assign into A and B (1, 2) types based on their genetic characteristics. CONCLUSION: In our study, we observed the genome-wide chromosomal aberrations of thymoma and identified significant gene sets with genetic variations related to thymoma subgroups, which might provide useful information for thymoma pathobiology.ope

Cost-effectiveness of chuna manual therapy and usual care, compared with usual care only for people with neck pain following traffic accidents: a multicenter randomized controlled trial

This is the first cost-effectiveness analysis of Chuna manual therapy (CMT) plus usual Korean traditional medicine for traffic accident victims using a randomized controlled trial. A total of 132 participants were equally allocated to the intervention group receiving 6–11 sessions of CMT plus usual Korean traditional medicine care for three weeks or usual care including acupuncture, cupping, herbal medicine, moxibustion, and traditional physiotherapy at three hospitals. At 12 weeks, from a healthcare perspective, the intervention group had significantly higher costs (mean (SD), $778 (435) vs.$618 (318); difference, $160; 95$15 to $289; p = 0.005). From a societal perspective, total costs were insignificantly lower in the intervention group (mean (SD),$1077 (1081) vs. $1146 (1485); difference,$−69; 95% CI, $−568 to$377; p = 0.761). The intervention group dominated, with significantly higher QALYs gained at lower overall cost with a 72% chance of being cost-effective. From a societal perspective, the intervention was cost-saving for individuals who had neck pain after car accidents, although it was not cost-effective from the healthcare perspective ($40,038 per QALY gained). Findings support use of CMT as an integrated care treatment for whiplash from a societal perspective. Further studies with larger sample sizes are needed to determine cost-effectiveness in other cultural contexts

Classification of rice (oryza sativa l. japonica nipponbare) immunophilins (fkbps, cyps) and expression patterns under water stress

<p>Abstract</p> <p>Background</p> <p>FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl <it>cis/trans </it>isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses.</p> <p>Results</p> <p>FKBP and CYP proteins in rice (<it>Oryza sativa </it>cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with <it>Arabidopsis </it>and <it>Chlamydomonas </it>or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of <it>Arabidopsis </it>IMMs. However, some genes were novel, did not match with those of <it>Arabidopsis </it>and <it>Chlamydomonas</it>, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein.</p> <p>Conclusion</p> <p>Like other green photosynthetic organisms such as <it>Arabidopsis </it>(23 FKBPs and 29 CYPs) and <it>Chlamydomonas </it>(23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, <it>Arabidopsis </it>and <it>Chlamydomonas</it>. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice.</p

Elemental compositions of smectites reveal detailed sediment provenance changes during glacial and interglacial periods: The Southern Drake Passage and Bellingshausen Sea, Antarctica

Variations in clay mineral assemblages have been widely used to understand changes in sediment provenance during glacial and interglacial periods. Smectite clay minerals, however, have a range of various elemental compositions that possibly originated from multiple different sources. Therefore, it might be crucial to distinguish the various types of smectites by analyzing their elemental composition in order to verify the sediment provenances with certainty. This hypothesis was tested for the clay mineral characteristics in a marine sediment core from the southern Drake Passage (GC05-DP02). Rare earth elements and ε Nd εNd data had previously indicated that fine grained detritus was supplied from the Weddell Sea to the core site during interglacial periods, when the sediments contained more Al-rich smectite (montmorillonite). Indeed, marine sediments collected close to the Larsen Ice Shelf on the eastern Antarctic Peninsula continental shelf, western Weddell Sea embayment, show more Al-rich smectite components as compared with other possible West Antarctic sources, such as the Ross Sea embayment or King George Island, South Shetland Islands. Furthermore, two types of smectite (Al-rich and Al-poor) were identified in core GC360 from the Bellingshausen Sea shelf, suggesting that during glacial periods some sediment is derived from subglacial erosion of underlying pre-Oligocene sedimentary strata containing predominantly Al-rich montmorillonite. This finding reveals different sources for smectites in sediments deposited at site GC360 during the last glacial period and during the present interglacial that show only minor differences in smectite contents. For the interglacial period, two groups of smectite with a wide range of Al-rich and Mg–Fe-rich were identified, which indicate delivery from two different sources: (1) the detritus with high contents of Mg–Fe-rich smectite supplied from Beethoven Peninsula, southwestern Alexander island and (2) the detritus with higher contents of Al-rich smectite (montmorillonite) possibly derived from the subglacial reworking of pre-Oligocene sedimentary strata. These results demonstrate that the elemental compositions of smectites can be used to differentiate the sources of smectites in marine sediments, which is an important tool to define sediment provenance in detail, when down-core changes observed in clay mineral assemblages are interpreted